Hi again,
the "non-pure" is from the comment in gaff.dat but I can see where this
is coming from. I think aromaticity is not a binary function but you
can assign somewthing like a "degree" of it. I would say this comes in
play when you, say, fuse an aromatic ring system with a ring system
that in itself is not aromatic but can conjugate with the aromatic
system.
In terms of an atom typed force field you have to make a decision which
one to assign or come up with your own if you think that neither are
optimal. On the other hand, will a simple force field catch this at
all? Is it really worth doing this?
Cheers,
Hannes.
On Tue, 28 Apr 2015 09:51:08 -0400
Robert Molt <rwmolt07.gmail.com> wrote:
> Hello,
>
> The definitions of the terms may be an issue here, for me. You
> describe cc as "non-pure aromatic system." I do not know what that
> means? In the original GAFF paper, it describes it as "inner sp2
> carbon on conjugated ring systems." I assume that means the fusion
> points (the "inner" part) on these conjugated rings, and hence there
> have to be exactly two.
>
> Regardless, if the system is sufficiently non-canonical that either
>
> a.) antechamber's specific atom designation subroutine called makes a
> "mistake" in designation
> b.) antechamber's specific atom designation subroutine does NOT make
> a mistake and parameters are missing
>
> then I should perhaps parameterize this on my own.
>
> On 4/28/15 9:29 AM, Hannes Loeffler wrote:
> > Hi,
> >
> > so you are saying that C1 and C2 are ca(=pure aromatic system) but
> > C3 and C4 within the same aromatic ring should be cc=(non-pure
> > aromatic system)? C5 is in the 5-ring and that may be what is
> > happening here: 6-ring pure aromatic, 5-ring not. You have to draw
> > the line somewhere. Of course, you can assign the atoms you think
> > are more suitable by hand or maybe even validate either set.
> >
> > It is not immediately obvious why either choice would be better than
> > the other. But I guess that's one of the limits of strict atom
> > typing. You could individually parameterise all terms or just the
> > ones in question, and possibly catch the chemistry better.
> >
> >
> > Cheers,
> > Hannes.
> >
> >
> > On Tue, 28 Apr 2015 09:03:24 -0400
> > Robert Molt <rwmolt07.gmail.com> wrote:
> >
> >> Good morning,
> >>
> >> I am saying that the two fusion points are both cc atoms, in terms
> >> of the GAFF atom types (or at leas they should be ). However, when
> >> you look at the table of atom types, there is only 1 cc-atom type.
> >>
> >> On 4/28/15 2:21 AM, hannes.loeffler.stfc.ac.uk wrote:
> >>> Hi,
> >>>
> >>> to understand how antechamber works is to first read the original
> >>> paper on it (I just don't have the reference here at the moment
> >>> but it must be cited in the manual) or best probably to read the
> >>> source code. If you run antechamber with -s 2 it tells what
> >>> "sub-programs" it is running (antechamber itself is mostly a
> >>> driver program). You would then see that the first one to run is
> >>> bondtype followed by atomtype.
> >>>
> >>> It is not clear to me, however, what your argument regarding the
> >>> atom types really is. If you consider the pyrimidine ring to be
> >>> aromatic then surely both C3 and C4 (the two fusion points) must
> >>> be the same, aromatic, atom type. You have drawn it that way
> >>> yourself.
> >>>
> >>> Cheers,
> >>> Hannes.
> >>>
> >>>
> >>> ________________________________________
> >>> From: Robert Molt [rwmolt07.gmail.com]
> >>> Sent: 28 April 2015 02:19
> >>> To: AMBER Mailing List
> >>> Subject: [AMBER] Antechamber Algorithm for Atom Type
> >>>
> >>> Good evening!
> >>>
> >>> I have a small, planar, aromatic organic molecule (C, N, H, O
> >>> atoms). I encountered a problem in parameterizing with GAFF; 4
> >>> dihedrals were not available. I tried to identify the four atoms
> >>> in the dihedral in my molecule, so I could just calculate the
> >>> torsional PES and add the parameters, and found some challenges.
> >>> I have attached a photo of the molecule in question.
> >>>
> >>> a.) Specifically, I was informed that I lacked 2 ca-ca-cc-h4
> >>> dihedral parameters and 2 ca-ca-cc-nd dihedral parameters by
> >>> xleap. However, when I look at the molecule, this designation
> >>> does not seem to make sense. There are 3 ca type carbons in the
> >>> molecule, if I understand properly, and none of them are adjacent
> >>> to one another; there is no cc adjacent to a h4. I /assume/,
> >>> perhaps erroneously, that the "best" choice in dihedrals to form
> >>> will be the ones that do not "jump" over atoms and thus go over
> >>> grater distances.
> >>>
> >>> b.) To confirm this, I examined ANTECHAMBER_AC.AC. It lists the
> >>> following table:
> >>>
> >>> ATOM 1 C1 MOL 1 -1.428 -1.191 -0.001
> >>> 0.000000 ca ATOM 2 N1 MOL 1 -2.039 0.009
> >>> 0.000 0.000000 nb ATOM 3 C2 MOL 1 -1.280
> >>> 1.097 -0.003 0.000000 ca ATOM 4 C3 MOL 1
> >>> 0.124 0.968 -0.003 0.000000 ca ATOM 5 C4 MOL
> >>> 1 0.596 -0.349 0.001 0.000000 ca ATOM 6 N2
> >>> MOL 1 -0.146 -1.465 0.002 0.000000 nb ATOM
> >>> 7 C5 MOL 1 1.299 1.764 -0.006 0.000000 cc
> >>> ATOM 8 H1 MOL 1 1.405 2.837 -0.014
> >>> 0.000000 h4
> >>> ATOM/usr/local/amber14/dat/leap/parm/gaff.dat 9 N3 MOL
> >>> 1 -1.900 2.297 -0.029 0.000000 nh ATOM 10 H2
> >>> MOL 1 -2.896 2.310 0.100 0.000000 hn ATOM
> >>> 11 H3 MOL 1 -1.380 3.137 0.142 0.000000 hn
> >>> ATOM 12 N4 MOL 1 2.371 1.010 -0.003
> >>> 0.000000 nd ATOM 13 N5 MOL 1 1.942
> >>> -0.275 0.002 0.000000 na ATOM 14 C6 MOL 1
> >>> 2.878 -1.373 0.005 0.000000 c3 ATOM 15 H4 MOL
> >>> 1 3.505 -1.324 0.893 0.000000 h1 ATOM 16 H5
> >>> MOL 1 2.301 -2.294 0.006 0.000000 h1 ATOM
> >>> 17 H6 MOL 1 3.506 -1.327 -0.883 0.000000 h1
> >>> ATOM 18 O1 MOL 1 -2.253 -2.246 -0.001 0.000000
> >>> oh ATOM 19 H7 MOL 1 -3.150 -1.895 -0.005
> >>> 0.000000 ho
> >>>
> >>> To me, this seemingly confirms my suspicion in a.) This table
> >>> lists there to be 4 ca's in the molecule and one cc. However,
> >>> pursuant to the original GAFF paper, I would say that there are 3
> >>> ca's and 2 cc's in the molecule (by my eye). Either that or I
> >>> deserve an F in organic chemistry, and hopefully Dr. Farrell is
> >>> not on this list-serv.
> >>>
> >>> c.) I am wondering if the antechamber algorithm for designating
> >>> atom types is meeting a pathological case? i.e., that it is
> >>> assigning incorrect atom types? I would guess that antechamber
> >>> uses a distance-based criterion for designating atom types? I am
> >>> having trouble finding out in the manual how antechamber takes xyz
> >>> coordinates read in to decide atom types?
> >>>
> >>> --
> >>> Dr. Robert Molt Jr.
> >>> r.molt.chemical.physics.gmail.com
> >>> Nigel Richards Research Group
> >>> Department of Chemistry & Chemical Biology
> >>> Indiana University-Purdue University Indianapolis
> >>> LD 326
> >>> 402 N. Blackford St.
> >>> Indianapolis, IN 46202
> >>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Apr 28 2015 - 07:30:02 PDT
